Linuxbrew-core: brew install gcc fails. Actually everything fails because installing glibc fails...
To help us debug your issue please explain:
- What you were trying to do (and why)
Install gcc because everything needs it. Also glibc.
- What happened (include command output)
aersoares81@myserver:~> brew install gcc
Updating Homebrew...
==> Installing dependencies for gcc: glibc, xz, m4, gmp, mpfr, libmpc, isl
==> Installing gcc dependency: glibc
==> Downloading https://ftp.gnu.org/gnu/glibc/glibc-2.23.tar.gz
Already downloaded: /home/aersoares81/.cache/Homebrew/glibc-2.23.tar.gz
==> ../configure --disable-debug --disable-dependency-tracking --disable-silent-rules --prefix=/home/aersoares81/.linuxbrew/Cellar/glibc/2.23 --enable-obsolete-rpc --wit
==> make
Last 15 lines from /home/aersoares81/.cache/Homebrew/Logs/glibc/02.make:
gcc-6 -B/home/aersoares81/.linuxbrew/opt/binutils/bin/ canonicalize.c -c -std=gnu11 -fgnu89-inline -O2 -Wall -Werror -Wundef -Wwrite-strings -fmerge-all-constants -frounding-math -g -Wstrict-prototypes -Wold-style-definition -fPIC -ftls-model=initial-exec -I../include -I/tmp/glibc-20170921-97952-cxeh2n/glibc-2.23/build/stdlib -I/tmp/glibc-20170921-97952-cxeh2n/glibc-2.23/build -I../sysdeps/unix/sysv/linux/x86_64/64 -I../sysdeps/unix/sysv/linux/x86_64 -I../sysdeps/unix/sysv/linux/x86 -I../sysdeps/unix/sysv/linux/wordsize-64 -I../sysdeps/x86_64/nptl -I../sysdeps/unix/sysv/linux/include -I../sysdeps/unix/sysv/linux -I../sysdeps/nptl -I../sysdeps/pthread -I../sysdeps/gnu -I../sysdeps/unix/inet -I../sysdeps/unix/sysv -I../sysdeps/unix/x86_64 -I../sysdeps/unix -I../sysdeps/posix -I../sysdeps/x86_64/64 -I../sysdeps/x86_64/fpu/multiarch -I../sysdeps/x86_64/fpu -I../sysdeps/x86/fpu/include -I../sysdeps/x86/fpu -I../sysdeps/x86_64/multiarch -I../sysdeps/x86_64 -I../sysdeps/x86 -I../sysdeps/ieee754/ldbl-96 -I../sysdeps/ieee754/dbl-64/wordsize-64 -I../sysdeps/ieee754/dbl-64 -I../sysdeps/ieee754/flt-32 -I../sysdeps/wordsize-64 -I../sysdeps/ieee754 -I../sysdeps/generic -I.. -I../libio -I. -nostdinc -isystem /usr/local/gcc-6.3.0/lib/gcc/x86_64-pc-linux-gnu/6.3.0/include -isystem /usr/local/gcc-6.3.0/lib/gcc/x86_64-pc-linux-gnu/6.3.0/include-fixed -isystem /home/aersoares81/.linuxbrew/opt/linux-headers/include -D_LIBC_REENTRANT -include /tmp/glibc-20170921-97952-cxeh2n/glibc-2.23/build/libc-modules.h -DMODULE_NAME=libc -include ../include/libc-symbols.h -DPIC -DSHARED -o /tmp/glibc-20170921-97952-cxeh2n/glibc-2.23/build/stdlib/canonicalize.os -MD -MP -MF /tmp/glibc-20170921-97952-cxeh2n/glibc-2.23/build/stdlib/canonicalize.os.dt -MT /tmp/glibc-20170921-97952-cxeh2n/glibc-2.23/build/stdlib/canonicalize.os
gcc-6 -B/home/aersoares81/.linuxbrew/opt/binutils/bin/ a64l.c -c -std=gnu11 -fgnu89-inline -O2 -Wall -Werror -Wundef -Wwrite-strings -fmerge-all-constants -frounding-math -g -Wstrict-prototypes -Wold-style-definition -fPIC -ftls-model=initial-exec -I../include -I/tmp/glibc-20170921-97952-cxeh2n/glibc-2.23/build/stdlib -I/tmp/glibc-20170921-97952-cxeh2n/glibc-2.23/build -I../sysdeps/unix/sysv/linux/x86_64/64 -I../sysdeps/unix/sysv/linux/x86_64 -I../sysdeps/unix/sysv/linux/x86 -I../sysdeps/unix/sysv/linux/wordsize-64 -I../sysdeps/x86_64/nptl -I../sysdeps/unix/sysv/linux/include -I../sysdeps/unix/sysv/linux -I../sysdeps/nptl -I../sysdeps/pthread -I../sysdeps/gnu -I../sysdeps/unix/inet -I../sysdeps/unix/sysv -I../sysdeps/unix/x86_64 -I../sysdeps/unix -I../sysdeps/posix -I../sysdeps/x86_64/64 -I../sysdeps/x86_64/fpu/multiarch -I../sysdeps/x86_64/fpu -I../sysdeps/x86/fpu/include -I../sysdeps/x86/fpu -I../sysdeps/x86_64/multiarch -I../sysdeps/x86_64 -I../sysdeps/x86 -I../sysdeps/ieee754/ldbl-96 -I../sysdeps/ieee754/dbl-64/wordsize-64 -I../sysdeps/ieee754/dbl-64 -I../sysdeps/ieee754/flt-32 -I../sysdeps/wordsize-64 -I../sysdeps/ieee754 -I../sysdeps/generic -I.. -I../libio -I. -nostdinc -isystem /usr/local/gcc-6.3.0/lib/gcc/x86_64-pc-linux-gnu/6.3.0/include -isystem /usr/local/gcc-6.3.0/lib/gcc/x86_64-pc-linux-gnu/6.3.0/include-fixed -isystem /home/aersoares81/.linuxbrew/opt/linux-headers/include -D_LIBC_REENTRANT -include /tmp/glibc-20170921-97952-cxeh2n/glibc-2.23/build/libc-modules.h -DMODULE_NAME=libc -include ../include/libc-symbols.h -DPIC -DSHARED -o /tmp/glibc-20170921-97952-cxeh2n/glibc-2.23/build/stdlib/a64l.os -MD -MP -MF /tmp/glibc-20170921-97952-cxeh2n/glibc-2.23/build/stdlib/a64l.os.dt -MT /tmp/glibc-20170921-97952-cxeh2n/glibc-2.23/build/stdlib/a64l.os
cc1: all warnings being treated as errors
make[2]: *** [/tmp/glibc-20170921-97952-cxeh2n/glibc-2.23/build/stdlib/setenv.o] Error 1
make[2]: *** Waiting for unfinished jobs....
setenv.c: In function ‘__unsetenv’:
setenv.c:279:6: error: suggest explicit braces to avoid ambiguous ‘else’ [-Werror=parentheses]
if (ep != NULL)
^
cc1: all warnings being treated as errors
make[2]: *** [/tmp/glibc-20170921-97952-cxeh2n/glibc-2.23/build/stdlib/setenv.os] Error 1
make[2]: Leaving directory `/tmp/glibc-20170921-97952-cxeh2n/glibc-2.23/stdlib'
make[1]: *** [stdlib/subdir_lib] Error 2
make[1]: Leaving directory `/tmp/glibc-20170921-97952-cxeh2n/glibc-2.23'
make: *** [all] Error 2
READ THIS: https://github.com/Linuxbrew/brew/blob/master/docs/Troubleshooting.md#troubleshooting
Please do not report this issue to Homebrew/brew or Homebrew/core, which support macOS only.
/home/aersoares81/.linuxbrew/Homebrew/Library/Homebrew/utils/github.rb:226:in `raise_api_error': curl failed! curl: (35) error:0D0C50A1:asn1 encoding routines:ASN1_item_verify:unknown message digest algorithm (GitHub::Error)
curl: (3) <url> malformed
from /home/aersoares81/.linuxbrew/Homebrew/Library/Homebrew/utils/github.rb:184:in `open'
from /home/aersoares81/.linuxbrew/Homebrew/Library/Homebrew/utils/github.rb:233:in `issues_matching'
from /home/aersoares81/.linuxbrew/Homebrew/Library/Homebrew/utils/github.rb:272:in `issues_for_formula'
from /home/aersoares81/.linuxbrew/Homebrew/Library/Homebrew/exceptions.rb:369:in `fetch_issues'
from /home/aersoares81/.linuxbrew/Homebrew/Library/Homebrew/exceptions.rb:365:in `issues'
from /home/aersoares81/.linuxbrew/Homebrew/Library/Homebrew/exceptions.rb:420:in `dump'
from /home/aersoares81/.linuxbrew/Homebrew/Library/Homebrew/brew.rb:133:in `rescue in <main>'
from /home/aersoares81/.linuxbrew/Homebrew/Library/Homebrew/brew.rb:26:in `<main>'
aersoares81@myserver:~>
- Other comments:
I also tried with HOMEBREW_CC=gcc-5 brew install gcc, and it also fails exactly the same way.
aersoares81
All 99 comments
Hi. On what Linux are you? You didn't fill out the issue template. Can you show us your brew config?
iMichka
on 22 Sep 2017
I have a similar problem. Everything involves gcc and glibc, and these two seem to be conflicting. The suggestion (below) to brew link --overwrite glibc, didn't help. The two relevant files turn out to be the same:
../Cellar/glibc/2.19_1/lib/libgcc_s.so.1
../Cellar/gcc/5.3.0/lib/libgcc_s.so.1
==> Upgrading bison
==> Installing dependencies for bison: glibc, gmp, mpfr, isl, gcc
==> Installing bison dependency: glibc
==> Downloading https://ftp.gnu.org/gnu/glibc/glibc-2.23.tar.gz
######################################################################## 100.0%
==> ../configure --disable-debug --disable-dependency-tracking --disable-silent-rules --prefix=/home/user/.linuxbrew/Cellar/glibc/2.23 --enable-obsolete-rpc --without-selinux --with-binutils=/hom
==> make
Last 15 lines from /home/user/.cache/Homebrew/Logs/glibc/02.make:
-o /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/cross-rpc_clntout.o -MMD -MP -MF /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/cross-rpc_clntout.o.dt -MT /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/cross-rpc_clntout.o -c
gcc-5 -B/home/user/.linuxbrew/opt/binutils/bin/ -D_RPC_THREAD_SAFE_ -D_GNU_SOURCE -DIS_IN_build -include /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/config.h rpc_tblout.c \
-o /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/cross-rpc_tblout.o -MMD -MP -MF /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/cross-rpc_tblout.o.dt -MT /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/cross-rpc_tblout.o -c
gcc-5 -B/home/user/.linuxbrew/opt/binutils/bin/ -D_RPC_THREAD_SAFE_ -D_GNU_SOURCE -DIS_IN_build -include /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/config.h rpc_sample.c \
-o /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/cross-rpc_sample.o -MMD -MP -MF /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/cross-rpc_sample.o.dt -MT /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/cross-rpc_sample.o -c
gcc-5 -B/home/user/.linuxbrew/opt/binutils/bin/ rpcgen.c -c -std=gnu11 -fgnu89-inline -O2 -Wall -Werror -Wundef -Wwrite-strings -fmerge-all-constants -frounding-math -g -Wstrict-prototypes -Wold-style-definition -D_RPC_THREAD_SAFE_ -I../include -I/home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc -I/home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build -I../sysdeps/unix/sysv/linux/x86_64/64 -I../sysdeps/unix/sysv/linux/x86_64 -I../sysdeps/unix/sysv/linux/x86 -I../sysdeps/unix/sysv/linux/wordsize-64 -I../sysdeps/x86_64/nptl -I../sysdeps/unix/sysv/linux/include -I../sysdeps/unix/sysv/linux -I../sysdeps/nptl -I../sysdeps/pthread -I../sysdeps/gnu -I../sysdeps/unix/inet -I../sysdeps/unix/sysv -I../sysdeps/unix/x86_64 -I../sysdeps/unix -I../sysdeps/posix -I../sysdeps/x86_64/64 -I../sysdeps/x86_64/fpu/multiarch -I../sysdeps/x86_64/fpu -I../sysdeps/x86/fpu/include -I../sysdeps/x86/fpu -I../sysdeps/x86_64/multiarch -I../sysdeps/x86_64 -I../sysdeps/x86 -I../sysdeps/ieee754/ldbl-96 -I../sysdeps/ieee754/dbl-64/wordsize-64 -I../sysdeps/ieee754/dbl-64 -I../sysdeps/ieee754/flt-32 -I../sysdeps/wordsize-64 -I../sysdeps/ieee754 -I../sysdeps/generic -I.. -I../libio -I. -nostdinc -isystem /home/user/.linuxbrew/Cellar/gcc/5.3.0/bin/../lib/gcc/x86_64-unknown-linux-gnu/5.3.0/include -isystem /home/user/.linuxbrew/Cellar/gcc/5.3.0/bin/../lib/gcc/x86_64-unknown-linux-gnu/5.3.0/include-fixed -isystem /home/user/.linuxbrew/opt/linux-headers/include -D_LIBC_REENTRANT -include /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/libc-modules.h -DMODULE_NAME=nonlib -include ../include/libc-symbols.h -D_RPC_THREAD_SAFE_ -o /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/rpcgen.o -MD -MP -MF /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/rpcgen.o.dt -MT /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/rpcgen.o
gcc-5 -B/home/user/.linuxbrew/opt/binutils/bin/ /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/cross-rpc_main.o /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/cross-rpc_hout.o /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/cross-rpc_cout.o /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/cross-rpc_parse.o /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/cross-rpc_scan.o /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/cross-rpc_util.o /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/cross-rpc_svcout.o /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/cross-rpc_clntout.o /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/cross-rpc_tblout.o /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/cross-rpc_sample.o -o /home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/cross-rpcgen
/home/user/.linuxbrew/opt/binutils/bin/ld: cannot find -lc
collect2: error: ld returned 1 exit status
make[2]: *** [/home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/build/sunrpc/cross-rpcgen] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory `/home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23/sunrpc'
make[1]: *** [sunrpc/others] Error 2
make[1]: Leaving directory `/home/user/tmp/glibc-20170930-5669-vp71k6/glibc-2.23'
make: *** [all] Error 2
Error: Could not symlink lib/libgcc_s.so.1
Target /home/user/.linuxbrew/lib/libgcc_s.so.1
is a symlink belonging to gcc. You can unlink it:
brew unlink gcc
To force the link and overwrite all conflicting files:
brew link --overwrite glibc
To list all files that would be deleted:
brew link --overwrite --dry-run glibc
DiagonalArg
on 30 Sep 2017
Same question as above:
Hi. On what Linux are you? You didn't fill out the issue template. Can you show us your brew config?
iMichka
on 30 Sep 2017
Ya, I'm on CentOS-7. Config is below, along with relevant doctor output. (Note that I have reported two more issues regarding a new install, also on CentOS-7 - indeed that same machine, only a different account - but that's not this one. This one was working well but went haywire on the latest upgrade.)
I would run brew gist-logs glibc and maybe also gcc, but running it places personal information up on github, and I can't find a way to get that info locally and edit that out. If you guys can fix this, it could be helpful. I'll open an issue.
This is brew config:
brew config
HOMEBREW_VERSION: 1.3.1
ORIGIN: https://github.com/Linuxbrew/brew
HEAD: 09208fb2af972b19a46f89ec8321232943e4c8d4
Last commit: 3 weeks ago
Core tap ORIGIN: https://github.com/Linuxbrew/homebrew-core
Core tap HEAD: 661746ca8282ef6899ab4f8f40ca54bbae5cc925
Core tap last commit: 27 hours ago
HOMEBREW_PREFIX: /home/user/.linuxbrew
HOMEBREW_REPOSITORY: /home/user/.linuxbrew
HOMEBREW_CELLAR: /home/user/.linuxbrew/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://linuxbrew.bintray.com
CPU: 40-core 64-bit broadwell
Homebrew Ruby: 2.0.0-p648 => /home/user/.linuxbrew/Library/Homebrew/vendor/portable-ruby/2.0.0-p648/bin/ruby
Clang: N/A
Git: 2.7.4 => /usr/bin/git
Perl: /usr/bin/perl
Python: /home/user/.linuxbrew/opt/python/libexec/bin/python => /home/user/.linuxbrew/Cellar/python/2.7.13_1/bin/python2.7
Ruby: /usr/bin/ruby
Java: openjdk version "1.8.0_144"
Kernel: Linux 3.10.0-514.16.1.el7.x86_64 x86_64 GNU/Linux
OS: CentOS Linux release 7.4.1708 (Core)
Host glibc: 2.17
/usr/bin/gcc: 4.8.5
glibc: 2.19_1
gcc: N/A
xorg: N/A
The only relevant thing appearing in brew doctor is right at the end:
Warning: You have unlinked kegs in your Cellar
Leaving kegs unlinked can lead to build-trouble and cause brews that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
gcc
Warning: Broken symlinks were found. Remove them with `brew prune`:
/home/dev/.linuxbrew/bin/c++
/home/dev/.linuxbrew/bin/cc
Warning: Some installed formula are missing dependencies.
You should `brew install` the missing dependencies:
brew install [email protected]
Run `brew missing` for more details.
Given the appearance of [email protected] in brew doctor, could this could be linked to this other problem (https://github.com/Linuxbrew/homebrew-core/issues/4538), which is appearing on my new install? (New, as in, a different account on the same machine.)
DiagonalArg
on 1 Oct 2017
I’ve got the same problem as @DiagonalArg (“cannot find -lc”) on Ubuntu 12.04.5. When checking where Homebrew’s/binutils ld looks for libraries (via ld --verbose | grep DIR), I find that it is linked to non-existent directories such as /home/linuxbrew/.linuxbrew/Cellar/binutils/2.29.1/lib64. The /home/linuxbrew/ part does not exist, and I have no idea where it is coming from.
For context, this was after several (long-existing) Homebrewed binaries suddenly stopped working with errors relating to glibc, and I tried fixing the problem by reinstalling glibc.
Here are my logs: https://gist.github.com/klmr/dc720b20733c31c2155af17afe5c52a4
klmr
on 3 Oct 2017
I've got the same problem! It's somehow got the wrong username.
ld --verbose | grep DIR
SEARCH_DIR("=/home/linuxbrew/.linuxbrew/Cellar/binutils/2.29.1/x86_64-pc-linux-gnu/lib64"); SEARCH_DIR("=/home/linuxbrew/.linuxbrew/Cellar/binutils/2.29.1/lib64"); SEARCH_DIR("=/usr/local/lib64"); SEARCH_DIR("=/lib64"); SEARCH_DIR("=/usr/lib64"); SEARCH_DIR("=/home/linuxbrew/.linuxbrew/Cellar/binutils/2.29.1/x86_64-pc-linux-gnu/lib"); SEARCH_DIR("=/home/linuxbrew/.linuxbrew/Cellar/binutils/2.29.1/lib"); SEARCH_DIR("=/usr/local/lib"); SEARCH_DIR("=/lib"); SEARCH_DIR("=/usr/lib");
The apparent wrong user name is a red herring. brew's Superenv tells binutils what the library search path should be.
sjackman
on 6 Oct 2017
It's looking for the file libc.so in the directory $(linuxbrew --prefix glibc)/lib. Please report the output of…
linuxbrew --prefix
linuxbrew --prefix glibc
ls -l $(linuxbrew --prefix glibc)
ls $(linuxbrew --prefix glibc)/lib/
$ brew --prefix
/home/user/.linuxbrew
$ brew --prefix glibc
/home/user/.linuxbrew/opt/glibc
$ ls -l $(brew --prefix glibc)
lrwxrwxrwx 1 user user 22 Oct 6 00:32 /home/user/.linuxbrew/opt/glibc -> ../Cellar/glibc/2.19_1
$ ls $(brew --prefix glibc)/lib/
audit libanl.so.1 libcrypt-2.19.so libgcc_s.so.1 libnsl.so.1 libnss_files.so libpcprofile.so librt-2.19.so libutil.so.1
crt1.o libBrokenLocale-2.19.so libcrypt.a libieee.a libnss_compat-2.19.so libnss_files.so.2 libpthread-2.19.so librt.a locale
crti.o libBrokenLocale.a libcrypt.so libm-2.19.so libnss_compat.so libnss_hesiod-2.19.so libpthread.a librt.so Mcrt1.o
crtn.o libBrokenLocale.so libcrypt.so.1 libm.a libnss_compat.so.2 libnss_hesiod.so libpthread_nonshared.a librt.so.1 Scrt1.o
gconv libBrokenLocale.so.1 libc.so libmcheck.a libnss_db-2.19.so libnss_hesiod.so.2 libpthread.so libSegFault.so
gcrt1.o libc-2.19.so libc.so.6 libmemusage.so libnss_db.so libnss_nis-2.19.so libpthread.so.0 libthread_db-1.0.so
ld-2.19.so libc.a libdl-2.19.so libm.so libnss_db.so.2 libnss_nisplus-2.19.so libresolv-2.19.so libthread_db.so
ld-linux-x86-64.so.2 libcidn-2.19.so libdl.a libm.so.6 libnss_dns-2.19.so libnss_nisplus.so libresolv.a libthread_db.so.1
libanl-2.19.so libcidn.so libdl.so libnsl-2.19.so libnss_dns.so libnss_nisplus.so.2 libresolv.so libutil-2.19.so
libanl.a libcidn.so.1 libdl.so.2 libnsl.a libnss_dns.so.2 libnss_nis.so libresolv.so.2 libutil.a
libanl.so libc_nonshared.a libg.a libnsl.so libnss_files-2.19.so libnss_nis.so.2 librpcsvc.a libutil.so
I should point out that those 3 last posts relate to an attempted install of a newer version of glibc that gives a similar but slightly different error:
$ brew upgrade glibc
==> Upgrading 1 outdated package, with result:
glibc 2.23
==> Upgrading glibc
==> Downloading https://ftp.gnu.org/gnu/glibc/glibc-2.23.tar.gz
Already downloaded: /home/user/.cache/Homebrew/glibc-2.23.tar.gz
==> ../configure --disable-debug --disable-dependency-tracking --disable-silent-rules --prefix=/home/user/.linuxbrew/Cellar/glibc/2.23 --enable-obsolete-rpc --without-selinux --with-binutils=/hom
==> make
Last 15 lines from /home/user/.cache/Homebrew/Logs/glibc/02.make:
-o /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc/cross-rpc_tblout.o -MMD -MP -MF /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc/cross-rpc_tblout.o.dt -MT /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc/cross-rpc_tblout.o -c
gcc-5 -B/home/user/.linuxbrew/opt/binutils/bin/ -D_RPC_THREAD_SAFE_ -D_GNU_SOURCE -DIS_IN_build -include /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/config.h rpc_sample.c \
-o /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc/cross-rpc_sample.o -MMD -MP -MF /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc/cross-rpc_sample.o.dt -MT /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc/cross-rpc_sample.o -c
gcc-5 -B/home/user/.linuxbrew/opt/binutils/bin/ rpcgen.c -c -std=gnu11 -fgnu89-inline -O2 -Wall -Werror -Wundef -Wwrite-strings -fmerge-all-constants -frounding-math -g -Wstrict-prototypes -Wold-style-definition -D_RPC_THREAD_SAFE_ -I../include -I/home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc -I/home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build -I../sysdeps/unix/sysv/linux/x86_64/64 -I../sysdeps/unix/sysv/linux/x86_64 -I../sysdeps/unix/sysv/linux/x86 -I../sysdeps/unix/sysv/linux/wordsize-64 -I../sysdeps/x86_64/nptl -I../sysdeps/unix/sysv/linux/include -I../sysdeps/unix/sysv/linux -I../sysdeps/nptl -I../sysdeps/pthread -I../sysdeps/gnu -I../sysdeps/unix/inet -I../sysdeps/unix/sysv -I../sysdeps/unix/x86_64 -I../sysdeps/unix -I../sysdeps/posix -I../sysdeps/x86_64/64 -I../sysdeps/x86_64/fpu/multiarch -I../sysdeps/x86_64/fpu -I../sysdeps/x86/fpu/include -I../sysdeps/x86/fpu -I../sysdeps/x86_64/multiarch -I../sysdeps/x86_64 -I../sysdeps/x86 -I../sysdeps/ieee754/ldbl-96 -I../sysdeps/ieee754/dbl-64/wordsize-64 -I../sysdeps/ieee754/dbl-64 -I../sysdeps/ieee754/flt-32 -I../sysdeps/wordsize-64 -I../sysdeps/ieee754 -I../sysdeps/generic -I.. -I../libio -I. -nostdinc -isystem /home/user/.linuxbrew/Cellar/gcc/5.3.0/bin/../lib/gcc/x86_64-unknown-linux-gnu/5.3.0/include -isystem /home/user/.linuxbrew/Cellar/gcc/5.3.0/bin/../lib/gcc/x86_64-unknown-linux-gnu/5.3.0/include-fixed -isystem /home/user/.linuxbrew/opt/linux-headers/include -D_LIBC_REENTRANT -include /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/libc-modules.h -DMODULE_NAME=nonlib -include ../include/libc-symbols.h -D_RPC_THREAD_SAFE_ -o /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc/rpcgen.o -MD -MP -MF /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc/rpcgen.o.dt -MT /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc/rpcgen.o
gcc-5 -B/home/user/.linuxbrew/opt/binutils/bin/ /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc/cross-rpc_main.o /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc/cross-rpc_hout.o /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc/cross-rpc_cout.o /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc/cross-rpc_parse.o /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc/cross-rpc_scan.o /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc/cross-rpc_util.o /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc/cross-rpc_svcout.o /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc/cross-rpc_clntout.o /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc/cross-rpc_tblout.o /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc/cross-rpc_sample.o -o /home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc/cross-rpcgen
/home/user/.linuxbrew/opt/binutils/bin/ld: cannot find -lgcc_s
/home/user/.linuxbrew/opt/binutils/bin/ld: cannot find -lc
/home/user/.linuxbrew/opt/binutils/bin/ld: cannot find -lgcc_s
collect2: error: ld returned 1 exit status
make[2]: *** [/home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/build/sunrpc/cross-rpcgen] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory `/home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23/sunrpc'
make[1]: *** [sunrpc/others] Error 2
make[1]: Leaving directory `/home/user/tmp/glibc-20171006-88014-59ol2h/glibc-2.23'
make: *** [all] Error 2
In addition, oddly, when I try to run that from other than my home directory, I get:
$ brew upgrade glibc
==> Upgrading 1 outdated package, with result:
glibc 2.23
==> Upgrading glibc
sudo: unable to resolve current working directory
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
==> Downloading https://ftp.gnu.org/gnu/glibc/glibc-2.23.tar.gz
Already downloaded: /home/user/.cache/Homebrew/glibc-2.23.tar.gz
Error: No such file or directory - getcwd
Here's the line of code that's supposed to tell it where to find -lc:
# Fix error ld: cannot find -lc when upgrading glibc and compiling with a brewed gcc.
ENV["BUILD_LDFLAGS"] = "-L#{opt_lib}" if opt_lib.directory?
https://github.com/Linuxbrew/homebrew-core/blob/master/Formula/glibc.rb#L101
sjackman
on 6 Oct 2017
That -L#{opt_lib} option doesn't seem to be making it into your link line though.
gcc-5 -B/home/user/.linuxbrew/opt/binutils/bin/ /home/user/tmp/glibc-20171006-179201-1igf3zt/glibc-2.23/build/sunrpc/cross-rpc_main.o /home/user/tmp/glibc-20171006-179201-1igf3zt/glibc-2.23/build/sunrpc/cross-rpc_hout.o /home/user/tmp/glibc-20171006-179201-1igf3zt/glibc-2.23/build/sunrpc/cross-rpc_cout.o /home/user/tmp/glibc-20171006-179201-1igf3zt/glibc-2.23/build/sunrpc/cross-rpc_parse.o /home/user/tmp/glibc-20171006-179201-1igf3zt/glibc-2.23/build/sunrpc/cross-rpc_scan.o /home/user/tmp/glibc-20171006-179201-1igf3zt/glibc-2.23/build/sunrpc/cross-rpc_util.o /home/user/tmp/glibc-20171006-179201-1igf3zt/glibc-2.23/build/sunrpc/cross-rpc_svcout.o /home/user/tmp/glibc-20171006-179201-1igf3zt/glibc-2.23/build/sunrpc/cross-rpc_clntout.o /home/user/tmp/glibc-20171006-179201-1igf3zt/glibc-2.23/build/sunrpc/cross-rpc_tblout.o /home/user/tmp/glibc-20171006-179201-1igf3zt/glibc-2.23/build/sunrpc/cross-rpc_sample.o -o /home/user/tmp/glibc-20171006-179201-1igf3zt/glibc-2.23/build/sunrpc/cross-rpcgen
/home/user/.linuxbrew/opt/binutils/bin/ld: cannot find -lgcc_s
/home/user/.linuxbrew/opt/binutils/bin/ld: cannot find -lc
Can you please report the output of…
brew irb <<EOS
Formula["gcc"].installed?
Formula["gcc"].version
EOS
For troubleshooting and possible a hack workaround, you could try brew edit glibc and change
if gcc.installed? && ENV.compiler == "gcc-" + gcc.version.to_s.split(".")[0]
to
if true
Just for completeness’ sake, my output is a bit difference since Linuxbrew’s glibc is missing:
⟩⟩⟩ brew --prefix
/lustre/scratch115/realdata/mdt2/teams/miska/users/kr15/linuxbrew
⟩⟩⟩ brew --prefix glibc
/lustre/scratch115/realdata/mdt2/teams/miska/users/kr15/linuxbrew/Cellar/glibc/2.23
⟩⟩⟩ ls -l $(brew --prefix glibc)
ls: cannot access /lustre/scratch115/realdata/mdt2/teams/miska/users/kr15/linuxbrew/Cellar/glibc/2.23: No such file or directory
The interactive console reports
Switch to inspect mode.
Formula["gcc"].installed?
true
Formula["gcc"].version
#<Version::FromURL:0x00000003407e70 @version="5.4.0">
Replacing the check in glibc.rb by if true as you mentioned doesn’t change the error, and no -L option is added to the relevant command line. In fact, Formula['glibc'].opt_lib.directory? is false when inspected in brew irb (not surprising: the path doesn’t exist, since the formula isn’t installed; see above).
klmr
on 6 Oct 2017
It says not installed, but brew list says it is.
$ brew irb <<EOS
> Formula["gcc"].installed?
> Formula["gcc"].version
> EOS
==> Interactive Homebrew Shell
Example commands available with: brew irb --examples
Switch to inspect mode.
Formula["gcc"].installed?
false
Formula["gcc"].version
#<Version::FromURL:0x000000038f8ce0 @version="5.4.0">
$ brew list
autoconf berkeley-db@4 colordiff gcc glibc gperf libatomic_ops libgcrypt libtool linux-headers nettle patchelf python3 sqlite unzip zlib
autogen binutils curl gdbm gmp guile libbsd libgpg-error libunistring m4 nmap pcre readline swig util-linux
automake bison dante gettext gnutls help2man libevent libmpc libxml2 mpfr openssl pkg-config speedtest_cli tmux w3m
bdw-gc bzip2 emacs glib gpatch isl libffi libtasn1 libxslt ncurses p11-kit python speedtest-cli transmission xz
$ printenv PATH
/home/user/.linuxbrew/sbin:/home/user/.linuxbrew/bin:/home/user/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin
$ ls .linuxbrew/bin/g*
g++-4.8 gdbus getopt gio-querymodules glibtool gobject-query gresource guile-config
gapplication gdbus-codegen gettext glib-compile-resources glibtoolize gold gsettings guile-snarf
gcc-4.8 gencat gettextize glib-compile-schemas gnutls-certtool gperf gtester guile-tools
gdbm_dump getconf gettext.sh glib-genmarshal gnutls-cli gpg-error gtester-report
gdbm_load getdefs gfortran-4.8 glib-gettextize gnutls-cli-debug gpg-error-config guild
gdbmtool getent gio glib-mkenums gnutls-serv gprof guile
$ ls -l gcc-4.8 g++-4.8
lrwxrwxrwx 1 user user 12 May 10 14:38 g++-4.8 -> /usr/bin/g++
lrwxrwxrwx 1 user user 12 May 10 14:38 gcc-4.8 -> /usr/bin/gcc
$ which gcc
/usr/bin/gcc
$ gcc --version
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)
It says not installed, but brew list says it is.
Please report the output of
brew list --versions gcc
brew info gcc
brew irb <<<'Formula["gcc"].installed?'
brew irb <<<'Formula["gcc"].any_version_installed?'
brew irb <<<'Formula["gcc"].linked?'
brew irb <<<'Formula["gcc"].optlinked?'
brew irb <<<'Formula["gcc"].prefix_linked?
@klmr I'd suggest trying a fresh install of Linuxbrew if that works for you. Follow these instructions for Ubuntu 12 Precise. https://github.com/Linuxbrew/brew/wiki/Ubuntu-12-Precise
sjackman
on 6 Oct 2017
@klmr Can you please report the output of ld --verbose | grep DIR? Do any of the listed directories contain the file libc.so? On Ubuntu it should be at /usr/lib/x86_64-linux-gnu/libc.so
sjackman
on 6 Oct 2017
$ brew list --versions gcc
gcc 5.3.0
$ brew info gcc
gcc: stable 5.4.0 (bottled), HEAD
GNU compiler collection
https://gcc.gnu.org/
/home/user/.linuxbrew/Cellar/gcc/5.3.0 (1,352 files, 253.0MB)
Poured from bottle on 2016-06-27 at 16:46:04
From: https://github.com/Linuxbrew/homebrew-core/blob/master/Formula/gcc.rb
==> Dependencies
Build: bzip2 ✔
Required: zlib ✔, gmp ✘, libmpc ✔, mpfr ✘, isl ✘
Recommended: glibc ✘
==> Options
--with-all-languages
Enable all compilers and languages, except Ada
--with-java
Build the gcj compiler
--with-jit
Build the jit compiler
--with-nls
Build with native language support (localization)
--without-fortran
Build without the gfortran compiler
--without-glibc
Build without glibc support
--HEAD
Install HEAD version
$ brew irb <<<'Formula["gcc"].installed?'
==> Interactive Homebrew Shell
Example commands available with: brew irb --examples
Switch to inspect mode.
Formula["gcc"].installed?
false
$ brew irb <<<'Formula["gcc"].any_version_installed?'
==> Interactive Homebrew Shell
Example commands available with: brew irb --examples
Switch to inspect mode.
Formula["gcc"].any_version_installed?
true
$ brew irb <<<'Formula["gcc"].linked?'
==> Interactive Homebrew Shell
Example commands available with: brew irb --examples
Switch to inspect mode.
Formula["gcc"].linked?
false
$ brew irb <<<'Formula["gcc"].optlinked?'
==> Interactive Homebrew Shell
Example commands available with: brew irb --examples
Switch to inspect mode.
Formula["gcc"].optlinked?
true
$ brew irb <<<'Formula["gcc"].prefix_linked?'
==> Interactive Homebrew Shell
Example commands available with: brew irb --examples
Switch to inspect mode.
Formula["gcc"].prefix_linked?
false
Seem like…
if gcc.installed? && ENV.compiler == "gcc-" + gcc.version.to_s.split(".")[0]
should be something like…
if gcc.any_version_installed? && ENV.compiler == "gcc-" + gcc.version.to_s.split(".")[0]
This logic looks pretty fragile though. Need a better way of determining if the selected compiler is provided by the host or brewed. Following the symlink of the compiler in the bin directory to see whether it's under brew --prefix is probably a better way to go.
sjackman
on 6 Oct 2017
Here's the line in the glibc Makefile where BUILD_LDFLAGS is added to the link line for cross-rpcgen: https://github.com/lattera/glibc/blob/master/sunrpc/Makefile#L169
$(objpfx)cross-rpcgen: $(cross-rpcgen-objs)
$(BUILD_CC) $^ $(BUILD_LDFLAGS) -o $@
Well, both fixes you suggest return the same error:
Error: The original GCC specs file is missing: /home/user/.linuxbrew/Cellar/gcc/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0/specs.orig
This file does exist, though:
~/.linuxbrew/Cellar/gcc/5.3.0/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/specs.orig
This clearly needs a better fix. As a workaround for now, copy the file
~/.linuxbrew/Cellar/gcc/5.3.0/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/specs.orig
to
~/.linuxbrew/Cellar/gcc/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0/specs.orig
ld --verbose | grep DIR | tr ';' '\n' | sed 's/ *SEARCH_DIR("=\(.*\)")/\1/' shows the following:
/home/linuxbrew/.linuxbrew/Cellar/binutils/2.29.1/x86_64-pc-linux-gnu/lib64
/home/linuxbrew/.linuxbrew/Cellar/binutils/2.29.1/lib64
/usr/local/lib64
/lib64
/usr/lib64
/home/linuxbrew/.linuxbrew/Cellar/binutils/2.29.1/x86_64-pc-linux-gnu/lib
/home/linuxbrew/.linuxbrew/Cellar/binutils/2.29.1/lib
/usr/local/lib
/lib
/usr/lib
Alas, none of these directories contains libc.so. I’ll try reinstalling Linuxbrew using the instructions you provided. Thanks!
klmr
on 8 Oct 2017
Huh. That is indeed a problem. Does the file exist at /usr/lib/x86_64-linux-gnu/libc.so?
If it does and you have write permission to any of the above directories, a workaround would be to symlink the above file to that location. If you don't, you could brew edit glibc and set the environment variable LIBRARY_PATH to /usr/lib/x86_64-linux-gnu/libc.so. Another option is to reinstall binutils from source: brew reinstall -s binutils
sjackman
on 8 Oct 2017
Hi @sjackman ,
I opened #4670 and was instructed to join the discussion.
I tried two suggestion from https://github.com/Linuxbrew/homebrew-core/issues/4388#issuecomment-335019916 but both failed.
On my machine, I found that libc.so is under /usr/lib64/libc.so.
Therefore, I added ENV["LIBRARY_PATH"] = "/usr/lib64" after https://github.com/Linuxbrew/homebrew-core/blob/master/Formula/glibc.rb#L92 but the same error occurred again.
I cannot install binutils from source. It failed during configure:
configure: WARNING: you should use --build, --host, --target
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether ln works... yes
checking whether ln -s works... yes
checking for a sed that does not truncate output... /bin/sed
checking for gawk... gawk
checking for gcc... gcc-5
checking for C compiler default output file name...
configure: error: in `/tmp/binutils-20171016-8733-lwnl7s/binutils-2.29.1':
configure: error: C compiler cannot create executables
See `config.log' for more details.
My system information is included in #4670.
Note that the linuxbrew claims that the minimal requirement is gcc 4.4 and linux 2.6.16, but I cannot install anything because current glibc-2.23 disable support of gcc 4.4: https://github.com/Linuxbrew/homebrew-core/commit/59b343a86689531bc59702e376654821f766b1c8#diff-eaf50caf94594abf81cb37c83a20e322. On my machine, I can only install glibc and gcc based on 6fb5dfd50895416bea3d00628b8d3b41fa1f4f32 before upgrading homebrew. Is it possible to provide older glibc for old compiler / linux?
wush978
on 16 Oct 2017
Hi, Wush. Consider installing Linuxbrew in /home/linuxbrew/.linuxbrew/ if possible so that you can use precompiled binary packages (known as bottles) for non-relocatable formula like glibc.
If you don't have sudo access, you could consider opening a ticket with your systems department to ask that they create a linuxbrew role account with home directory /home/linuxbrew for the purpose of sharing software that is used by your group.
OS: CentOS release 6.8 (Final) (Final)
https://gist.github.com/anonymous/c080e352a764614b8d5f3bc045c85eb0#file-00-config-out-L21
If it's an option for you, try a fresh installation of Linuxbrew following these instructions:
https://github.com/Linuxbrew/brew/wiki/CentOS6
My apologies for the hassle.
Is it possible to provide older glibc for old compiler / linux?
We do in fact provide an older version of GCC 4.9 [email protected], whose binary bottle requires glibc ≥ 2.19 to use.
Linuxbrew doesn't currently handle the situation well when the host OS provides GCC < 4.7, and you want to install in your home directory. One possible solution is to install a new version of gcc from source first, before installing glibc.
sjackman
on 16 Oct 2017
What is the state of this? I would like to know if there is some action that we need to take to help people to get this to run.
I have sometimes a hard time to follow all the use cases with the different glibc/gcc versions. We have some wiki pages here https://github.com/Linuxbrew/brew/wiki that may need some updates and more details. Could somebody summarise a little bit the situation?
iMichka
on 24 Oct 2017
Installing in /home/linuxbrew/.linuxbrew should work just fine, regardless of the host system.
Installing elsewhere when the host provides gcc < 4.7 can be a bit tricky, because glibc requires gcc ≥ 4.7 to compiler from source.
We have workarounds for the common distributions in https://github.com/Linuxbrew/brew/wiki
sjackman
on 25 Oct 2017
@iMichka - I don't know if @sjackman is talking about a new install, but I'm at gcc 4.8 and I was not able to upgrade without the problems you see above.
DiagonalArg
on 26 Oct 2017
Same here. gcc 5.4 and cannot install glibc, and linux brew is installed at $HOME/.linuxbrew
paulhybryant
on 14 Nov 2017
@paulhybryant Please report brew gist-logs glibc (or whichever formula failed to build).
sjackman
on 15 Nov 2017
The issue is fixed by
brew rm gcc
brew reinstall -s binutils
brew install glibc
Glad to hear that you got it working. Do you know why it was necessary to rebuild binutils from source? I take it the bottle didn't work for you. The bottle for binutils is meant to work on any system.
sjackman
on 17 Nov 2017
I forgot from which thread I saw that but it should be one of the issue in
linuxbrew.
Before I did the described steps, brew install glibc or brew install wget
will fail with
error like ld: cannot find -lc or ld: cannot find -lutil.
Rebuilding binutils from source solves that problem.
paulhybryant
on 19 Nov 2017
@paulhybryant Your workaround did not work for me. I'm still unable to install glibc.
HOMEBREW_VERSION: >1.2.0 (shallow or no git repository)
ORIGIN: https://github.com/Linuxbrew/brew
HEAD: 3aecdc02948da03bb9feab52643eecfc02d903d5
Last commit: 29 hours ago
Core tap ORIGIN: https://github.com/Linuxbrew/homebrew-core
Core tap HEAD: dbe8816162b3aeafc62fc551205e3bd937577d2b
Core tap last commit: 6 hours ago
HOMEBREW_PREFIX: /home/hg299/.linuxbrew
HOMEBREW_REPOSITORY: /home/hg299/.linuxbrew/Homebrew
HOMEBREW_CELLAR: /home/hg299/.linuxbrew/Cellar
HOMEBREW_CACHE: /home/hg299/.cache/Homebrew
HOMEBREW_CELLAR: /home/hg299/.linuxbrew/Cellar
HOMEBREW_DEV_CMD_RUN: 1
HOMEBREW_GIT_CONFIG_FILE: /home/hg299/.linuxbrew/Homebrew/.git/config
HOMEBREW_PREFIX: /home/hg299/.linuxbrew
HOMEBREW_REPOSITORY: /home/hg299/.linuxbrew/Homebrew
CPU: octa-core 64-bit nehalem
Homebrew Ruby: 2.3.3 => /home/hg299/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.3/bin/ruby
Clang: N/A
Git: 2.9.5 => /home/hg299/usr/local/bin/git
Curl: 7.37.0 => /usr/bin/curl
Perl: /usr/bin/perl
Python: /usr/bin/python => /usr/bin/python2.7
Ruby: /usr/bin/ruby => /usr/bin/ruby.ruby2.1
Java: openjdk version "1.8.0_151"
Kernel: Linux 4.4.92-31-default x86_64 GNU/Linux
OS: openSUSE Leap 42.3 (n/a)
Host glibc: 2.22
/usr/bin/gcc: 4.8.5
glibc: N/A
gcc: N/A
xorg: N/A
~> brew install glibc
==> Downloading https://ftp.gnu.org/gnu/glibc/glibc-2.23.tar.gz
Already downloaded: /home/hg299/.cache/Homebrew/glibc-2.23.tar.gz
==> ../configure --disable-debug --disable-dependency-tracking --disable-silent-rules --prefix=/hom
==> make
==> make install
.....
rm -f /tmp/glibc-20171129-11566-12lc21e/glibc-2.23/build/elf/symlink.list
test ! -x /tmp/glibc-20171129-11566-12lc21e/glibc-2.23/build/elf/ldconfig || LC_ALL=C \
/tmp/glibc-20171129-11566-12lc21e/glibc-2.23/build/elf/ldconfig \
/home/hg299/.linuxbrew/Cellar/glibc/2.23/lib /home/hg299/.linuxbrew/Cellar/glibc/2.23/lib64
/tmp/glibc-20171129-11566-12lc21e/glibc-2.23/build/elf/ldconfig: Warning: ignoring configuration file that cannot be opened: /home/hg299/.linuxbrew/Cellar/glibc/2.23/etc/ld.so.conf: No such file or directory
make[1]: Leaving directory '/tmp/glibc-20171129-11566-12lc21e/glibc-2.23'
==> Kept temporary files
Temporary files retained at /tmp/glibc-20171129-11566-12lc21e
Error: Failure while executing: /home/hg299/.linuxbrew/Cellar/glibc/2.23/bin/ldd /home/hg299/.linuxbrew/Cellar/glibc/2.23/bin/gencat
not a dynamic executable
hangong
on 29 Nov 2017
HOMEBREW_VERSION: >1.2.0
That's super old. Could you update first?
iMichka
on 29 Nov 2017
@iMichka I was given the 1.2 version when the system did not have a git (maybe this is another bug). So, I compiled and installed one. And, I removed the old brew and had a fresh install (when git was available).
But I still got the same error. BTW, I did not have the root permission.
~> brew install -d glibc
....
==> Downloading https://ftp.gnu.org/gnu/glibc/glibc-2.23.tar.gz
Already downloaded: /home/hg299/.cache/Homebrew/glibc-2.23.tar.gz
==> ../configure --disable-debug --disable-dependency-tracking --disable-silent-rules --prefix=/hom
==> make
==> make install
==> Kept temporary files
Temporary files retained at /tmp/glibc-20171129-13893-q6p0z
Error: Failure while executing: /home/hg299/.linuxbrew/Cellar/glibc/2.23/bin/ldd /home/hg299/.linuxbrew/Cellar/glibc/2.23/bin/gencat
not a dynamic executable
/home/hg299/.linuxbrew/Homebrew/Library/Homebrew/debrew.rb:11:in `raise'
/home/hg299/.linuxbrew/Homebrew/Library/Homebrew/os/linux/elf.rb:68:in `initialize'
/home/hg299/.linuxbrew/Homebrew/Library/Homebrew/os/linux/elf.rb:109:in `new'
/home/hg299/.linuxbrew/Homebrew/Library/Homebrew/os/linux/elf.rb:109:in `metadata'
...
```
~> brew config
HOMEBREW_VERSION: 1.3.8
ORIGIN: https://github.com/Linuxbrew/brew
HEAD: fbc16c2b5b62baea3e63bac5bf2e82f1e75126df
Last commit: 8 days ago
Core tap ORIGIN: https://github.com/Linuxbrew/homebrew-core
Core tap HEAD: dbe8816162b3aeafc62fc551205e3bd937577d2b
Core tap last commit: 16 hours ago
HOMEBREW_PREFIX: /home/hg299/.linuxbrew
HOMEBREW_REPOSITORY: /home/hg299/.linuxbrew/Homebrew
HOMEBREW_CELLAR: /home/hg299/.linuxbrew/Cellar
HOMEBREW_CACHE: /home/hg299/.cache/Homebrew
HOMEBREW_CELLAR: /home/hg299/.linuxbrew/Cellar
HOMEBREW_GIT_CONFIG_FILE: /home/hg299/.linuxbrew/Homebrew/.git/config
HOMEBREW_PREFIX: /home/hg299/.linuxbrew
HOMEBREW_REPOSITORY: /home/hg299/.linuxbrew/Homebrew
CPU: octa-core 64-bit nehalem
Homebrew Ruby: 2.3.3 => /home/hg299/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.3/bin/ruby
Clang: N/A
Git: 2.9.5 => /home/hg299/usr/local/bin/git
Curl: 7.37.0 => /usr/bin/curl
Perl: /usr/bin/perl
Python: /usr/bin/python => /usr/bin/python2.7
Ruby: /usr/bin/ruby => /usr/bin/ruby.ruby2.1
Java: openjdk version "1.8.0_151"
Kernel: Linux 4.4.92-31-default x86_64 GNU/Linux
OS: openSUSE Leap 42.3 (n/a)
Host glibc: 2.22
/usr/bin/gcc: 4.8.5
glibc: N/A
gcc: N/A
~> brew list
binutils bzip2 gmp linux-headers m4 patchelf xz zlib
````
I have also tried this. No luck.
Thanks.
hangong
on 29 Nov 2017
Consider installing Linuxbrew in /home/linuxbrew/.linuxbrew/ if possible so that you can use precompiled binary packages (known as bottles) for non-relocatable formula like glibc.
If it's an option for you, you could open a ticket with your systems department to ask that they create a linuxbrew role account with home directory /home/linuxbrew for the purpose of sharing software that is used by your group.
The precompiled binary bottles of non-relocatable bottles can only be used if you install in /home/linuxbrew/.linuxbrew, otherwise they have to be built from source. See the documentation below, but wherever it reads /usr/local, which is for macOS, read instead /home/linuxbrew/.linuxbrew.
- http://docs.brew.sh/Installation.html#alternative-installs
- http://docs.brew.sh/FAQ.html#why-do-you-compile-everything
- http://docs.brew.sh/Bottles.html#cellar-cellar
sjackman
on 29 Nov 2017
Error: Failure while executing: /home/hg299/.linuxbrew/Cellar/glibc/2.23/bin/ldd /home/hg299/.linuxbrew/Cellar/glibc/2.23/bin/gencat
not a dynamic executable
For troubleshooting, try…
brew install -dv glibc
/home/hg299/.linuxbrew/Cellar/glibc/2.23/bin/ldd /home/hg299/.linuxbrew/Cellar/glibc/2.23/bin/gencat
file /home/hg299/.linuxbrew/Cellar/glibc/2.23/bin/gencat
/home/hg299/.linuxbrew/Cellar/glibc/2.23/bin/gencat --version
@sjackman Thanks for the reminder. The error codes are actually the same as my previous post.
brew install -dv glibc
....
rm -f /tmp/glibc-20171129-23339-139dmxg/glibc-2.23/build/stubs.h
/tmp/glibc-20171129-23339-139dmxg/glibc-2.23/build/elf/sln /tmp/glibc-20171129-23339-139dmxg/glibc-2.23/build/elf/symlink.list
rm -f /tmp/glibc-20171129-23339-139dmxg/glibc-2.23/build/elf/symlink.list
test ! -x /tmp/glibc-20171129-23339-139dmxg/glibc-2.23/build/elf/ldconfig || LC_ALL=C \
/tmp/glibc-20171129-23339-139dmxg/glibc-2.23/build/elf/ldconfig \
/home/hg299/.linuxbrew/Cellar/glibc/2.23/lib /home/hg299/.linuxbrew/Cellar/glibc/2.23/lib64
/tmp/glibc-20171129-23339-139dmxg/glibc-2.23/build/elf/ldconfig: Warning: ignoring configuration file that cannot be opened: /home/hg299/.linuxbrew/Cellar/glibc/2.23/etc/ld.so.conf: No such file or directory
make[1]: Leaving directory '/tmp/glibc-20171129-23339-139dmxg/glibc-2.23'
==> Kept temporary files
Temporary files retained at /tmp/glibc-20171129-23339-139dmxg
Error: Failure while executing: /home/hg299/.linuxbrew/Cellar/glibc/2.23/bin/ldd /home/hg299/.linuxbrew/Cellar/glibc/2.23/bin/gencat
not a dynamic executable
/home/hg299/.linuxbrew/Homebrew/Library/Homebrew/debrew.rb:11:in `raise'
/home/hg299/.linuxbrew/Homebrew/Library/Homebrew/os/linux/elf.rb:68:in `initialize'
/home/hg299/.linuxbrew/Homebrew/Library/Homebrew/os/linux/elf.rb:109:in `new'
/home/hg299/.linuxbrew/Homebrew/Library/Homebrew/os/linux/elf.rb:109:in `metadata'
/home/hg299/.linuxbrew/Homebrew/Library/Homebrew/os/linux/elf.rb:120:in `dynamically_linked_libraries'
.....
~> brew config
HOMEBREW_VERSION: 1.3.8
ORIGIN: https://github.com/Linuxbrew/brew
HEAD: fbc16c2b5b62baea3e63bac5bf2e82f1e75126df
Last commit: 8 days ago
Core tap ORIGIN: https://github.com/Linuxbrew/homebrew-core
Core tap HEAD: a034ee119aabb6777a727e50a63da2f142ab735c
Core tap last commit: 2 hours ago
HOMEBREW_PREFIX: /home/hg299/.linuxbrew
HOMEBREW_REPOSITORY: /home/hg299/.linuxbrew/Homebrew
HOMEBREW_CELLAR: /home/hg299/.linuxbrew/Cellar
HOMEBREW_CACHE: /home/hg299/.cache/Homebrew
HOMEBREW_CELLAR: /home/hg299/.linuxbrew/Cellar
HOMEBREW_GIT_CONFIG_FILE: /home/hg299/.linuxbrew/Homebrew/.git/config
HOMEBREW_PREFIX: /home/hg299/.linuxbrew
HOMEBREW_REPOSITORY: /home/hg299/.linuxbrew/Homebrew
CPU: octa-core 64-bit nehalem
Homebrew Ruby: 2.3.3 => /home/hg299/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.3/bin/ruby
Clang: N/A
Git: 2.9.5 => /home/hg299/usr/local/bin/git
Curl: 7.37.0 => /usr/bin/curl
Perl: /usr/bin/perl
Python: /usr/bin/python => /usr/bin/python2.7
Ruby: /usr/bin/ruby => /usr/bin/ruby.ruby2.1
Java: openjdk version "1.8.0_151"
Kernel: Linux 4.4.92-31-default x86_64 GNU/Linux
OS: openSUSE Leap 42.3 (n/a)
Host glibc: 2.22
/usr/bin/gcc: 4.8.5
glibc: N/A
gcc: N/A
xorg: N/A
~> brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!
Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and what additional flags to use when
compiling and linking.
Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew provided
script of the same name. We found the following "config" scripts:
/usr/bin/X11/libpng16-config
/usr/bin/X11/ncursesw6-config
/usr/bin/X11/python-config
/usr/bin/X11/MagickCore-config
/usr/bin/X11/python3.4m-config
/usr/bin/X11/xslt-config
/usr/bin/X11/ggz-config
/usr/bin/X11/libpng-config
/usr/bin/X11/curl-config
/usr/bin/X11/xine-config
/usr/bin/X11/pcre-config
/usr/bin/X11/antlr-config
/usr/bin/X11/pkg-config
/usr/bin/X11/isolinux-config
/usr/bin/X11/python2.7-config
/usr/bin/X11/MagickWand-config
/usr/bin/X11/ncursesw5-config
/usr/bin/X11/cups-config
/usr/bin/X11/libassuan-config
/usr/bin/X11/icu-config
/usr/bin/X11/Wand-config
/usr/bin/X11/apu-1-config
/usr/bin/X11/apr-1-config
/usr/bin/X11/wv2-config
/usr/bin/X11/ncurses5-config
/usr/bin/X11/Magick-config
/usr/bin/X11/libusb-config
/usr/bin/X11/freetype-config
/usr/bin/X11/pspell-config
/usr/bin/X11/kde4-config
/usr/bin/X11/gphoto2-config
/usr/bin/X11/x86_64-suse-linux-gnu-pkg-config
/usr/bin/X11/gphoto2-port-config
/usr/bin/X11/python3-config
/usr/bin/X11/python3.4-config
/usr/bin/X11/gpg-error-config
/usr/bin/X11/ncurses6-config
/usr/bin/X11/xml2-config
/usr/bin/X11/python2-config
/usr/bin/X11/libart2-config
/usr/bin/X11/libgcrypt-config
/usr/bin/X11/sdl-config
/usr/bin/X11/gpgme-config
/usr/bin/X11/kf5-config
/usr/lib/mit/bin/krb5-config
I was hoping that brew -dv would give a prompt where you could inspect further what's awry with the gencat executable. Sadly no prompt it seems.
As hack workaround, try commenting out this line:
raise ErrorDuringExecution, "#{command.join(" ")}\n#{libs.join("\n")}" unless $CHILD_STATUS.success?
https://github.com/Linuxbrew/brew/blob/master/Library/Homebrew/os/linux/elf.rb#L68
Then set export HOMEBREW_NO_AUTO_UPDATE=1 and try brew install again.
After glibc is installed, we can inspect what's up with gencat.
sjackman
on 29 Nov 2017
@sjackman Thanks. Glibc is installed. However, its post-installation failed.
==> make install
==> /home/hg299/.linuxbrew/Cellar/glibc/2.23/bin/localedef -i en_GB -f UTF-8 en_GB.UTF-8
Last 15 lines from /home/hg299/.cache/Homebrew/Logs/glibc/post_install.01.localedef:
2017-11-29 20:44:52 +0000
/home/hg299/.linuxbrew/Cellar/glibc/2.23/bin/localedef
-i
en_GB
-f
UTF-8
en_GB.UTF-8
cannot create temporary file: /home/hg299/.linuxbrew/Cellar/glibc/2.23/lib64/locale/locale-archive.yLJQvd: No such file or directory
Warning: The post-install step did not complete successfully
You can try again using `brew postinstall glibc`
==> Summary
🍺 /home/hg299/.linuxbrew/Cellar/glibc/2.23: 1,413 files, 88.2MB, built in 4 minutes 13 seconds
I tried to run "brew postinstall glibc" again. It reported the same error.
UPDTAE: So I manually created the directory .linuxbrew/Cellar/glibc/2.23/lib64/locale/. The post-installation finished with no errors. But gcc was still stuck.
gcc was then successfully installed. However, it did not pass the test.
~> brew test gcc
Testing gcc
==> /home/hg299/.linuxbrew/Cellar/gcc/5.4.0/bin/gcc-5 -o hello-c hello-c.c
Last 15 lines from /home/hg299/.cache/Homebrew/Logs/gcc/test.01.gcc-5:
2017-11-29 20:51:00 +0000
/home/hg299/.linuxbrew/Cellar/gcc/5.4.0/bin/gcc-5
-o
hello-c
hello-c.c
/usr/bin/X11/ld: cannot find -lc
collect2: error: ld returned 1 exit status
Error: gcc: failed
Failed executing: /home/hg299/.linuxbrew/Cellar/gcc/5.4.0/bin/gcc-5 -o hello-c hello-c.c
/home/hg299/.linuxbrew/Homebrew/Library/Homebrew/formula.rb:1796:in `block in system'
/home/hg299/.linuxbrew/Homebrew/Library/Homebrew/formula.rb:1734:in `open'
/home/hg299/.linuxbrew/Homebrew/Library/Homebrew/formula.rb:1734:in `system'
/home/hg299/.linuxbrew/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/gcc.rb:299:in `block in <class:Gcc>'
When I tried to compile a helloworld.c with gcc.
~> gcc helloworld.c -o a
/home/hg299/.linuxbrew/bin/ld: cannot find -lc
collect2: error: ld returned 1 exit status
Try…
brew postinstall gcc
and check that /home/hg299/.linuxbrew/lib/libc.so exists.
sjackman
on 29 Nov 2017
@sjackman post-installed gcc with no errors. but it still failed the test (cannot find -lc).
~> brew postinstall gcc
==> Postinstalling gcc
==> Creating the GCC specs file: /home/hg299/.linuxbrew/Cellar/gcc/5.4.0/bin/../lib/gcc/x86_64-unkn
> brew test gcc
Testing gcc
==> /home/hg299/.linuxbrew/Cellar/gcc/5.4.0/bin/gcc-5 -o hello-c hello-c.c
Last 15 lines from /home/hg299/.cache/Homebrew/Logs/gcc/test.01.gcc-5:
2017-11-29 21:33:05 +0000
/home/hg299/.linuxbrew/Cellar/gcc/5.4.0/bin/gcc-5
-o
hello-c
hello-c.c
/usr/bin/X11/ld: cannot find -lc
collect2: error: ld returned 1 exit status
Error: gcc: failed
BTW, I already had these in my bash_profile
export XDG_DATA_DIRS="/home/hg299/.linuxbrew/share:$XDG_DATA_DIRS"
export MANPATH="/home/hg299/.linuxbrew/share/man:$HOME/usr/local/share/man:$MANPATH"
export INFOPATH="/home/hg299/.linuxbrew/share/info:$INFOPATH"
export PATH='/home/hg299/.linuxbrew/bin:/home/hg299/.linuxbrew/sbin':"$PATH"
/usr/bin/X11/ld: cannot find -lc
That's a strange path for ld. Do you have binutils installed by brew? Please report…
which -a ld
ld --verison
brew install binutils
Yes, it was already there. I installed it by brew install -s binutils
OK, let me rollback. I executed the following steps first.
~> brew remove glibc
~> brew remove binutils
~> brew install binutils
~> brew install glibc
~> mkdir -p /home/hg299/.linuxbrew/Cellar/glibc/2.23/lib64/locale/
~> brew postinstall glibc
~> brew install gcc
~> brew postinstall gcc
The above commands were executed with no errors (with the aforementioned workarounds)
~> brew test gcc
...
/usr/bin/X11/ld: cannot find -lc
collect2: error: ld returned 1 exit status
Error: gcc: failed
~> which -a ld
/home/hg299/.linuxbrew/bin/ld
/usr/bin/ld
/usr/bin/X11/ld
~> ld -v
GNU ld (GNU Binutils) 2.29.1
~> brew install binutils
Warning: binutils 2.29.1 is already installed
~> brew list
binutils bzip2 gcc glibc gmp isl libmpc linux-headers m4 mpfr patchelf xz zlib
~> gcc helloworld.c
/home/hg299/.linuxbrew/bin/ld: cannot find -lc
collect2: error: ld returned 1 exit status
Report the output of…
brew postinstall gcc -v
The last few lines of the specs file should look like this:
*cpp_unique_options:
+ -isystem /home/sjackman/.linuxbrew/include
*link_libgcc:
-nostdlib -L/home/sjackman/.linuxbrew/Cellar/gcc/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0 -L/home/sjackman/.linuxbrew/lib
*link:
+ --dynamic-linker /home/sjackman/.linuxbrew/lib/ld.so -rpath /home/sjackman/.linuxbrew/lib
~> brew postinstall gcc -dv
/home/hg299/.linuxbrew/Homebrew/Library/Homebrew/brew.rb (Formulary::FormulaLoader): loading /home/hg299/.linuxbrew/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/gcc.rb
/home/hg299/.linuxbrew/Homebrew/Library/Homebrew/brew.rb (Formulary::FormulaLoader): loading /home/hg299/.linuxbrew/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/glibc.rb
==> Postinstalling gcc
/home/hg299/.linuxbrew/Homebrew/Library/Homebrew/postinstall.rb (Formulary::FromPathLoader): loading /home/hg299/.linuxbrew/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/gcc.rb
/home/hg299/.linuxbrew/Homebrew/Library/Homebrew/postinstall.rb (Formulary::FormulaLoader): loading /home/hg299/.linuxbrew/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/glibc.rb
==> Creating the GCC specs file: /home/hg299/.linuxbrew/Cellar/gcc/5.4.0/bin/../lib/gcc/x86_64-unknown-linux-gnu/5.4.0/specs
The list few lines:
*cpp_unique_options:
+ -isystem /home/hg299/.linuxbrew/include
*link_libgcc:
-nostdlib -L/home/hg299/.linuxbrew/Cellar/gcc/5.4.0/lib/gcc/x86_64-unknown-linux-gnu/5.4.0 -L/home/hg299/.linuxbrew/lib
*link:
+ --dynamic-linker /home/hg299/.linuxbrew/lib/ld.so -rpath /home/hg299/.linuxbrew/lib
I'm running out of ideas. Sorry, Han.
sjackman
on 30 Nov 2017
Thanks @sjackman . I suspect this is caused by something else.
There is a missing step to generate "~/.linuxbrew/Cellar/glibc/2.23/etc/ld.so.conf" and run ldconfig for the cache.
However when I run ldconfig, I got:
ldconfig: file /home/hg299/.linuxbrew/lib/libgmp.so.10 is truncated
ldconfig: file /home/hg299/.linuxbrew/lib/libz.so is truncated
ldconfig: file /home/hg299/.linuxbrew/lib/libbz2.so is truncated
ldconfig: file /home/hg299/.linuxbrew/lib/libz.so.1.2.11 is truncated
ldconfig: file /home/hg299/.linuxbrew/lib/libisl.so.15.3.0 is truncated
ldconfig: file /home/hg299/.linuxbrew/lib/libgmpxx.so.4 is truncated
ldconfig: file /home/hg299/.linuxbrew/lib/libbz2.so.1 is truncated
ldconfig: file /home/hg299/.linuxbrew/lib/libgmpxx.so is truncated
ldconfig: file /home/hg299/.linuxbrew/lib/libmpfr.so.4.1.6 is truncated
ldconfig: file /home/hg299/.linuxbrew/lib/libgmp.so is truncated
ldconfig: file /home/hg299/.linuxbrew/lib/libisl.so is truncated
ldconfig: file /home/hg299/.linuxbrew/lib/libbz2.so.1.0 is truncated
ldconfig: file /home/hg299/.linuxbrew/lib/libmpc.so is truncated
ldconfig: file /home/hg299/.linuxbrew/lib/libmpfr.so.4 is truncated
.....
everything is truncated. What does that imply? The compiled libs are not compatible with the brew base? Interesting. I can confirm that the ldconfig is the brew's.
hangong
on 30 Nov 2017
Linuxbrew uses RPATH embedded in each executable rather than ld.so.conf. It's not necessary to run ldconfig. The executables are modified with patchelf after they're installed. Most tools are fine with that, but ldconfig is not. It thinks they're "truncated".
sjackman
on 30 Nov 2017
Thanks anyway. I'm giving up. So the conclusion is that the current brew does not work on "openSUSE Leap 42.3" with a non-root account. I have seen similar posts somewhere else before.
hangong
on 30 Nov 2017
I've successfully installed Linuxbrew as a non-root user on an OpenSUSE 42.3 Leap system using Docker. So, I'm afraid that I'm not able to replicate your issue. It appears to be unique to your system.
Here's the Dockerfile that I used for a user with sudo access:
https://github.com/Linuxbrew/docker/blob/master/opensuse/Dockerfile
Here's a Dockerfile script for a user that does not have sudo access:
FROM opensuse:leap
LABEL maintainer="Shaun Jackman <[email protected]>"
RUN zypper --non-interactive install curl git glibc-i18ndata gcc glibc-locale make sudo tar which \
&& localedef -i en_US -f UTF-8 en_US.UTF-8 \
&& useradd -m -s /bin/bash user
USER user
WORKDIR /home/user
ENV PATH=/home/user/.linuxbrew/bin:/home/user/.linuxbrew/sbin:$PATH \
SHELL=/bin/bash \
USER=user
RUN yes | sh -c "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/install/master/install.sh)" \
&& brew config
CMD ["/bin/bash"]
Run these commands to test it:
docker build -t linuxbrew-opensuse .
docker run -it linuxbrew-opensuse
brew install hello
brew test glibc gcc hello
@sjackman Would this be helpful for you to find out what went wrong?
strace gcc helloworld.c
https://paste.fedoraproject.org/paste/uFvOPuXLRYsCQZF4xy3X7A
Actually, I tried the same thing on another cluster (Cent OS 6). I got the similar issue that ldd always tells me *** is not a dynamic executable.
hangong
on 2 Dec 2017
I'm afraid that I don't have the time available to help troubleshoot. Sorry!
sjackman
on 2 Dec 2017
This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.
![stale[bot] picture](https://avatars3.githubusercontent.com/in/1724?v=4&s=40)
stale[bot]
on 23 Dec 2017
@hangong
I got the similar issue that ldd always tells me * is not a dynamic executable.
Though I don't know what was causing it, this particular error message should not occur with Linuxbrew 1.3.9.
sjackman
on 23 Dec 2017
This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.
stale[bot]
on 13 Jan 2018
@sjackman I tried your suggestion for installing to /home/linuxbrew to get around glibc failing (in my case it's failing due to the new compilers giving warnings for glibc and all warnings being treated as errors). Here is my gist-log here for the attempt at install glibc, https://gist.github.com/anonymous/5568abacbd36e5c29cc486131cc89322
Is there something else I need to do to have glibc install as bottle?
Thanks!
Nick
nickjhathaway
on 20 Jan 2018
You're installing to /data/home/linuxbrew/.linuxbrew
https://gist.github.com/anonymous/5568abacbd36e5c29cc486131cc89322#file-00-config-out-L8
It ought to be /home/linuxbrew/.linuxbrew
sjackman
on 20 Jan 2018
gcc-7 -B/data/home/linuxbrew/.linuxbrew/opt/binutils/bin/ ../sysdeps/wordsize-64/strtoll.c -c -std=gnu11 -fgnu89-inline -fno-stack-protector -O2 -Wall -Werror -Wundef -Wwrite-strings -fmerge-all-constants -frounding-math -g -Wstrict-prototypes -Wold-style-definition -ftls-model=initial-exec -U_FORTIFY_SOURCE -I../include -I/tmp/glibc-20180120-12853-2vz38y/glibc-2.23/build/stdlib -I/tmp/glibc-20180120-12853-2vz38y/glibc-2.23/build -I../sysdeps/unix/sysv/linux/x86_64/64 -I../sysdeps/unix/sysv/linux/x86_64 -I../sysdeps/unix/sysv/linux/x86 -I../sysdeps/unix/sysv/linux/wordsize-64 -I../sysdeps/x86_64/nptl -I../sysdeps/unix/sysv/linux/include -I../sysdeps/unix/sysv/linux -I../sysdeps/nptl -I../sysdeps/pthread -I../sysdeps/gnu -I../sysdeps/unix/inet -I../sysdeps/unix/sysv -I../sysdeps/unix/x86_64 -I../sysdeps/unix -I../sysdeps/posix -I../sysdeps/x86_64/64 -I../sysdeps/x86_64/fpu/multiarch -I../sysdeps/x86_64/fpu -I../sysdeps/x86/fpu/include -I../sysdeps/x86/fpu -I../sysdeps/x86_64/multiarch -I../sysdeps/x86_64 -I../sysdeps/x86 -I../sysdeps/ieee754/ldbl-96 -I../sysdeps/ieee754/dbl-64/wordsize-64 -I../sysdeps/ieee754/dbl-64 -I../sysdeps/ieee754/flt-32 -I../sysdeps/wordsize-64 -I../sysdeps/ieee754 -I../sysdeps/generic -I.. -I../libio -I. -nostdinc -isystem /usr/lib/gcc/x86_64-linux-gnu/7/include -isystem /usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -isystem /data/home/linuxbrew/.linuxbrew/opt/linux-headers/include -D_LIBC_REENTRANT -include /tmp/glibc-20180120-12853-2vz38y/glibc-2.23/build/libc-modules.h -DMODULE_NAME=libc -include ../include/libc-symbols.h -o /tmp/glibc-20180120-12853-2vz38y/glibc-2.23/build/stdlib/strtoll.o -MD -MP -MF /tmp/glibc-20180120-12853-2vz38y/glibc-2.23/build/stdlib/strtoll.o.dt -MT /tmp/glibc-20180120-12853-2vz38y/glibc-2.23/build/stdlib/strtoll.o
setenv.c: In function ‘__unsetenv’:
setenv.c:279:6: error: suggest explicit braces to avoid ambiguous ‘else’ [-Werror=dangling-else]
if (ep != NULL)
https://gist.github.com/anonymous/5568abacbd36e5c29cc486131cc89322#file-02-make-L887
Well that's frustrating. You can edit the glibc formula with brew edit glibc to add the option --disable-werror to ./configure.
See https://www.gnu.org/software/libc/manual/html_node/Configuring-and-compiling.html
sjackman
on 20 Jan 2018
/usr/bin/gcc: 6.3.0
https://gist.github.com/anonymous/5568abacbd36e5c29cc486131cc89322#file-00-config-out-L28
You can try…
brew install glibc --cc=gcc-6
OS: Ubuntu 14.04.5 LTS (trusty)
Host glibc: 2.19
/usr/bin/gcc: 6.3.0
The default compiler on Ubuntu 14.04 is usually gcc-4.8. It's unusual that /usr/bin/gcc points to 6.3.0 on your system.
sjackman
on 20 Jan 2018
Excellent, @sjackman thanks so much for the speedy response! The warnings started to appear with gcc-6 it seems so the following did the trick.
brew install glibc --cc=gcc-5
And yes the main person who admins the server is a tad ridiculous, he moved /home/ to /data/home and then created a symlink from /data/home to /home, not sure why and so I'm sure there are several other quirky things as well on the system like the default compiler being different.
Thanks for the fix!
nickjhathaway
on 20 Jan 2018
Glad that you got it working, Nick! Since you have that symlink of /home to /data/home, you could also use
brew install --force-bottle foo
to install whichever package foo that you want, including glibc. You could even set up an alias:
alias install='brew install --force-bottle'
install foo
Excellent, good to know
nickjhathaway
on 20 Jan 2018
I am trying to install git in $HOME without root access or gcc (and $HOME != /user/linuxbrew) on Ubuntu 14.04. But it refuses to install glibc with Error: The following formula:
glibc
cannot be installed as a binary package and must be built from source.
I have read through the comments here, and tried several of the suggestions with no success. It is not clear whether there is any consensus whether it is possible or not. What is the final verdict? Impossible?
ziggurism
on 27 Mar 2018
I'm not sure why that's an error for you. I believe it should be a warning. In any case, try…
brew install -s glibc
brew install gcc
brew install git
~$ brew install -s glibc
Error: The following flag:
--build-from-source
requires building tools, but none are installed.
Install Clang or brew install gcc
I am trying to install git in $HOME without root access
Installing in $HOME requires a compiler, and it looks as though you do not have a compiler installed.
If you have root access, install in /home/linuxbrew/.linuxbrew, which does not require a compiler.
If you do not have root access, contact your system administrator and ask them to install a compiler.
Alternatively, open a ticket with your systems department to ask that they create a linuxbrew role account with home directory /home/linuxbrew for the purpose of sharing software that is used by your group.
sjackman
on 27 Mar 2018
Ok so you're saying it's impossible to install linuxbrew in $HOME with no root access and no gcc when $HOME is not /home/linuxbrew, is that right?
ziggurism
on 27 Mar 2018
Yes, that's correct. If you're installing in $HOME with no root access, no compiler, and you have glibc < 2.23, it's (probably) impossible. If you had glibc ≥ 2.23 (Ubuntu 14.04 or later) you could use the precompiled gcc bottle.
The precompiled GCC bottle is compiled against glibc 2.23, and you have glibc 2.19. Before the precompiled GCC bottle can be used, you have to install glibc. The glibc bottle is not relocatable, so it must be compiled from source when installing in your home directory, which requires a compiler.
If you're technically savvy and are willing to do some troubleshooting on your own, you can try…
brew install --force-bottle glibc
brew install gcc
brew install git
I don't know how technically savvy I am, but for the sake of science:
~$ brew install --force-bottle glibc
==> Installing dependencies for glibc: patchelf, zlib, binutils, linux-headers
==> Installing glibc dependency: patchelf
==> Downloading https://linuxbrew.bintray.com/bottles/patchelf-0.9_1.x86_64_linux.bottle.tar.gz
Already downloaded: /home/user/.cache/Homebrew/patchelf-0.9_1.x86_64_linux.bottle.tar.gz
==> Pouring patchelf-0.9_1.x86_64_linux.bottle.tar.gz
🍺 /home/user/.linuxbrew/Cellar/patchelf/0.9_1: 6 files, 1.2MB
==> Installing glibc dependency: zlib
==> Downloading https://linuxbrew.bintray.com/bottles/zlib-1.2.11.x86_64_linux.bottle.tar.gz
Already downloaded: /home/user/.cache/Homebrew/zlib-1.2.11.x86_64_linux.bottle.tar.gz
==> Pouring zlib-1.2.11.x86_64_linux.bottle.tar.gz
🍺 /home/user/.linuxbrew/Cellar/zlib/1.2.11: 12 files, 423.5KB
==> Installing glibc dependency: binutils
==> Downloading https://linuxbrew.bintray.com/bottles/binutils-2.30.x86_64_linux.bottle.tar.gz
Already downloaded: /home/user/.cache/Homebrew/binutils-2.30.x86_64_linux.bottle.tar.gz
==> Pouring binutils-2.30.x86_64_linux.bottle.tar.gz
🍺 /home/user/.linuxbrew/Cellar/binutils/2.30: 5,002 files, 222.2MB
==> Installing glibc dependency: linux-headers
==> Downloading https://linuxbrew.bintray.com/bottles/linux-headers-4.4.80.x86_64_linux.bottle.tar.gz
Already downloaded: /home/user/.cache/Homebrew/linux-headers-4.4.80.x86_64_linux.bottle.tar.gz
==> Pouring linux-headers-4.4.80.x86_64_linux.bottle.tar.gz
🍺 /home/user/.linuxbrew/Cellar/linux-headers/4.4.80: 772 files, 3.7MB
==> Installing glibc
==> Downloading https://linuxbrew.bintray.com/bottles/glibc-2.23.x86_64_linux.bottle.tar.gz
Already downloaded: /home/user/.cache/Homebrew/glibc-2.23.x86_64_linux.bottle.tar.gz
==> Pouring glibc-2.23.x86_64_linux.bottle.tar.gz
==> Installing locale data for en_US.UTF-8
==> /home/user/.linuxbrew/Cellar/glibc/2.23/bin/localedef -i en_US -f UTF-8 en_US.UTF-8
Last 15 lines from /home/user/.cache/Homebrew/Logs/glibc/post_install.01.localedef:
2018-03-27 10:02:27 -0700
/home/user/.linuxbrew/Cellar/glibc/2.23/bin/localedef
-i
en_US
-f
UTF-8
en_US.UTF-8
Warning: The post-install step did not complete successfully
You can try again using `brew postinstall glibc`
and then
~$ brew postinstall glibc
==> Postinstalling glibc
==> Installing locale data for en_US.UTF-8
==> /home/user/.linuxbrew/Cellar/glibc/2.23/bin/localedef -i en_US -f UTF-8 en_US.UTF-8
Last 15 lines from /home/user/.cache/Homebrew/Logs/glibc/post_install.01.localedef:
2018-03-27 10:06:47 -0700
/home/user/.linuxbrew/Cellar/glibc/2.23/bin/localedef
-i
en_US
-f
UTF-8
en_US.UTF-8
READ THIS: https://github.com/Linuxbrew/brew/wiki/troubleshooting
Please do not report this issue to Homebrew/brew or Homebrew/core, which support macOS only.
These open issues may also help:
brew install glibc fails looking for gcc 5.5.0_1 specs file https://github.com/Linuxbrew/homebrew-core/issues/5707
Error: No developer tools installed.
Install Clang or brew install gcc
For science! 🔬 ☣️ :atom:
Try running…
/home/user/.linuxbrew/Cellar/glibc/2.23/bin/localedef -i en_US -f UTF-8 en_US.UTF-8
brew install gcc
brew install git
So much for tech-savvy, lol. Here I get an error I do not understand at all:
$ /home/user/.linuxbrew/Cellar/glibc/2.23/bin/localedef
-bash: /home/user/.linuxbrew/Cellar/glibc/2.23/bin/localedef: No such file or directory
even though
$ ls -la /home/user/.linuxbrew/Cellar/glibc/2.23/bin/localedef
-r-xr-xr-x 1 user user 1434696 Feb 18 2016 /home/user/.linuxbrew/Cellar/glibc/2.23/bin/localedef
returns successfully. The file is definitely there, with executable permissions, but I cannot find it or execute it?
ziggurism
on 28 Mar 2018
That means that the dynamic linker is missing. Report…
patchelf --print-interpreter ~/.linuxbrew/Cellar/glibc/2.23/bin/localedef
ls -l $(patchelf --print-interpreter ~/.linuxbrew/Cellar/glibc/2.23/bin/localedef)
ls -l ~/.linuxbrew/lib/ld.so
realpath ~/.linuxbrew/lib/ld.so
I remember now. glibc is intentionally not relocated because relocating its dynamic libraries breaks it. Relocating its executables would probably be fine. In any case, you can ignore this error for now and continue on with…
brew install gcc
brew install git
First:
$ patchelf --print-interpreter ~/.linuxbrew/Cellar/glibc/2.23/bin/localedef
/home/linuxbrew/.linuxbrew/Cellar/glibc/2.23/lib/ld-linux-x86-64.so.2
$ ls -l ~/.linuxbrew/lib/ld.so
lrwxrwxrwx 1 user user 67 Mar 27 10:06 /home/user/.linuxbrew/lib/ld.so -> /home/user/.linuxbrew/Cellar/glibc/2.23/lib/ld-linux-x86-64.so.2
md5-2d8fb914f29147ecd1a320015b54b845
$ realpath ~/.linuxbrew/lib/ld.so
The program 'realpath' is currently not installed. To run 'realpath' please ask your administrator to install the package 'realpath'
md5-0a3c7cb577ac036010b9e69b4362cc9d
$ brew install gcc
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 1 tap (homebrew/core).
==> New Formulae
php-cs-fixer
==> Updated Formulae
amber clinfo git-ftp kompose [email protected] php teleport
ant cockroach gtk-doc kubernetes-cli media-info picard-tools terragrunt
apibuilder-cli convmv headphones languagetool mediaconch planck typescript
artifactory dartsim heroku laszip nuxeo pmd vala
azure-cli dcm2niix hwloc libatomic_ops openssl pygobject3 vnu
ballerina dovecot ircd-hybrid libqalculate [email protected] redis webpack
buku fades jbig2enc lmod packer rom-tools yq
bzt fonttools joplin mame paket rust zstd
caddy geth kedge mariadb pdal sbt
==> Installing dependencies for gcc: gmp, mpfr, libmpc, [email protected]
==> Installing gcc dependency: gmp
==> Downloading https://linuxbrew.bintray.com/bottles/gmp-6.1.2_2.x86_64_linux.bottle.tar.gz
Already downloaded: /home/user/.cache/Homebrew/gmp-6.1.2_2.x86_64_linux.bottle.tar.gz
==> Pouring gmp-6.1.2_2.x86_64_linux.bottle.tar.gz
Error: Failure while executing: ["readelf", "-d", "/home/user/.linuxbrew/Cellar/gmp/6.1.2_2/lib/libgmp.so.10.3.2"]
Warning: Bottle installation failed: building from source.
Error: The following formula:
gmp
cannot be installed as a binary package and must be built from source.
Install Clang or brew install gcc
This seems like a new error than before. Have we succcessfully installed glibc, only to have same failure with gmp?
ziggurism
on 29 Mar 2018
Well, we're making progress. Please report…
which -a readelf
readelf --version
readelf -d /home/user/.linuxbrew/Cellar/gmp/6.1.2_2/lib/libgmp.so.10.3.2
which -a file
file --version
file /home/user/.linuxbrew/Cellar/gmp/6.1.2_2/lib/libgmp.so.10.3.2
$ which -a readelf
/home/user/.linuxbrew/bin/readelf
/home/user/.linuxbrew/bin/readelf
why twice?
$ readelf --version
GNU readelf (GNU Binutils) 2.30
$ ls /home/user/.linuxbrew/Cellar/gmp
ls: cannot access /home/user/.linuxbrew/Cellar/gmp: No such file or directory
so obviously the other references to the gmp shared object also fail.
And finally
$ which -a file
/usr/bin/file
and
$ file --version
file-5.14
magic file from /etc/magic:/usr/share/misc/magic
Report…
HOMEBREW_STDERR=1 brew install -v gmp
$ HOMEBREW_STDERR=1 brew install -v gmp
==> Downloading https://linuxbrew.bintray.com/bottles/gmp-6.1.2_2.x86_64_linux.bottle.tar.gz
Already downloaded: /home/user/.cache/Homebrew/gmp-6.1.2_2.x86_64_linux.bottle.tar.gz
==> Verifying gmp-6.1.2_2.x86_64_linux.bottle.tar.gz checksum
==> Pouring gmp-6.1.2_2.x86_64_linux.bottle.tar.gz
tar xzf /home/user/.cache/Homebrew/gmp-6.1.2_2.x86_64_linux.bottle.tar.gz
/home/user/.linuxbrew/opt/patchelf/bin/patchelf --force-rpath --set-rpath /home/user/.linuxbrew/Cellar/gmp/6.1.2_2/lib:/home/user/.linuxbrew/lib /home/user/.linuxbrew/Cellar/gmp/6.1.2_2/lib/libgmp.so.10.3.2
/home/user/.linuxbrew/opt/patchelf/bin/patchelf --force-rpath --set-rpath /home/user/.linuxbrew/Cellar/gmp/6.1.2_2/lib:/home/user/.linuxbrew/lib /home/user/.linuxbrew/Cellar/gmp/6.1.2_2/lib/libgmpxx.so.4.5.2
brew: command not found: readelf
Error: Failure while executing: ["readelf", "-d", "/home/user/.linuxbrew/Cellar/gmp/6.1.2_2/lib/libgmp.so.10.3.2"]
Warning: Bottle installation failed: building from source.
Error: The following formula:
gmp
cannot be installed as a binary package and must be built from source.
Install Clang or brew install gcc
But readelf is present and in my PATH as previously reported, so what gives...?
ziggurism
on 29 Mar 2018
brew resets the PATH to /usr/bin:/bin by default. In this case it should display Please install either readelf (from binutils) or file. Odd that it's not displaying this error message.
Try…
HOMEBREW_NO_ENV_FILTERING=1 brew install gcc git
Definite progress! The last command appears to have installed gcc successfully, although it still barfs on git,
Error: The following formula:
git
cannot be installed as a binary package and must be built from source.
I'm assuming something like brew install --build-from-source git is next, but I'll let you confirm first.
And the full output from last brew is on gist.
ziggurism
on 29 Mar 2018
That's a strange error. It should install git from source using the gcc compiler that we just installed, Yep, the next step is brew install -s git.
sjackman
on 29 Mar 2018
Well brew install -s git did
==> Installing dependencies for git: gdbm, berkeley-db, libbsd, expat, perl, openssl, pkg-config, curl
==> Installing git dependency: gdbm
==> Downloading https://linuxbrew.bintray.com/bottles/gdbm-1.14.1_1.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring gdbm-1.14.1_1.x86_64_linux.bottle.tar.gz
Error: Failure while executing: ["readelf", "-d", "/home/user/.linuxbrew/Cellar/gdbm/1.14.1_1/bin/gdbm_dump"]
Warning: Bottle installation failed: building from source.
==> Downloading https://ftp.gnu.org/gnu/gdbm/gdbm-1.14.1.tar.gz
######################################################################## 100.0%
==> ./configure --disable-silent-rules --without-readline --prefix=/home/user/.linuxbrew/Cellar/gdbm/1.14.1
==> make install
Last 15 lines from /home/user/.cache/Homebrew/Logs/gdbm/02.make:
2018-03-29 08:20:26 -0700
make
install
READ THIS: https://github.com/Linuxbrew/brew/wiki/troubleshooting
Please do not report this issue to Homebrew/brew or Homebrew/core, which support macOS only.
recognizing that readelf error, I then did HOMEBREW_NO_ENV_FILTERING=1 brew install --build-from-source git and got
So make is not installed? Is that not part of the gcc package? No, I guess it's its own brew package. Ok, so I then tried HOMEBREW_NO_ENV_FILTERING=1 brew install --build-from-source make. No error, but no install either...
==> Downloading https://ftp.gnu.org/gnu/make/make-4.2.1.tar.bz2
######################################################################## 100.0%
==> ./configure --prefix=/home/user/.linuxbrew/Cellar/make/4.2.1_1
==> make install
Last 15 lines from /home/user/.cache/Homebrew/Logs/make/02.make:
2018-03-29 08:23:56 -0700
make
install
READ THIS: https://github.com/Linuxbrew/brew/wiki/troubleshooting
Please do not report this issue to Homebrew/brew or Homebrew/core, which support macOS only.
$ which make
<no result>
$ ls ~/.linuxbrew/bin/make
ls: cannot access /home/user/.linuxbrew/bin/make: No such file or directory
Please report brew gist-logs make or if that fails, post the contents of the directory /home/user/.cache/Homebrew/Logs/make/ or at least the file 02.make at https://gist.github.com
Try…
export HOMEBREW_NO_ENV_FILTERING=1
brew install --force-bottle make
brew install git
I couldn't get brew gist-logs to authenticate.
But I copy-pasted 02.make log to this gist. As you see, there is no error message. It seems to just set some environment variables and then conclude silently. Like it didn't even try to compile.
So anyway... --force-bottle worked. It's in the middle of a lengthy compilation of some dependency, perl, I think, looks like it may take a while to finish. But at this point I'm pretty sure it's going to install git.
ziggurism
on 29 Mar 2018
make install
https://gist.github.com/ziggurism/2f80111cdf909dffae55f317fc55c767#file-02-make-L3-L4
The first thing that brew install -s make does is try to run make. 😜😶🤔
Glad that you're making progress!
sjackman
on 29 Mar 2018
oh whoops! I guess I was expecting it at the bottom, or I dunno. So anyway, what do you make of that 02.make file? Should there be a message reporting success or failure of the install?
In other news, git and all dependencies finished compiling. You're a freakin wizard, dude! I thought it was impossible because precompiled glibc had hardcoded pathnames. You did some black magic, I dunno.
ziggurism
on 29 Mar 2018
Yeah, there should be an error, saying something like bash: make: command not found. I'm not sure why that error message is not printed.
Hah! I'm a ninja wizard. We need ninja and wizard emoji.
You should be mostly okay, but there may be some glibc features that don't work for you. localedef for example still isn't working for you (which is fixable with some patchelf hackery).
Now that we got to the end of this, I'm curious. What sort of system are you on that you're running Ubuntu 14, with no root access, and no compiler? The first two are pretty common on academic systems, but they would typically have a compiler installed. It's unusual not to have a compiler.
sjackman
on 29 Mar 2018
So to sum up, the key steps were
$ patchelf --print-interpreter ~/.linuxbrew/Cellar/glibc/2.23/bin/localedefto getglibcto install,HOMEBREW_NO_ENV_FILTERING=1 brew install --force-bottle <whatever bottles are still being bad>for the rest.
By the way, thank you so much, sjackman, for the extremely extensive support on this.
ziggurism
on 29 Mar 2018
patchelf --print-interpreter ~/.linuxbrew/Cellar/glibc/2.23/bin/localedef
That command doesn't do anything. =) It was just for troubleshooting. The key was…
HOMEBREW_NO_ENV_FILTERING=1 brew install --force-bottle glibc make
and ignore the brew postinstall glibc failure like a 🤠
sjackman
on 29 Mar 2018
By the way, thank you so much, sjackman, for the extremely extensive support on this.
Happy to help! 😄
sjackman
on 29 Mar 2018
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Happy to help! 😄